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| 2684 | </dd> | 2684 | </dd> |
| 2685 | <dt><a·href="jebl/evolution/coalescent/Intervals.html#getSampleCount()"·class="member-name-link">getSampleCount()</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/Intervals.html"·title="class·in·jebl.evolution.coalescent">Intervals</a></dt> | 2685 | <dt><a·href="jebl/evolution/coalescent/Intervals.html#getSampleCount()"·class="member-name-link">getSampleCount()</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/Intervals.html"·title="class·in·jebl.evolution.coalescent">Intervals</a></dt> |
| 2686 | <dd> </dd> | 2686 | <dd> </dd> |
| 2687 | <dt><a·href="jebl/evolution/align/Align.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 2687 | <dt><a·href="jebl/evolution/align/Align.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 2688 | <dd> </dd> | 2688 | <dd> </dd> |
| 2689 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> | 2689 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 2690 | <dd> </dd> | 2690 | <dd> </dd> |
| 2691 | <dt><a·href="jebl/evolution/align/ | 2691 | <dt><a·href="jebl/evolution/align/MaximalSegmentPair.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/MaximalSegmentPair.html"·title="class·in·jebl.evolution.align">MaximalSegmentPair</a></dt> |
| 2692 | <dd> </dd> | 2692 | <dd> </dd> |
| 2693 | <dt><a·href="jebl/evolution/align/BartonSternberg.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/BartonSternberg.html"·title="class·in·jebl.evolution.align">BartonSternberg</a></dt> | 2693 | <dt><a·href="jebl/evolution/align/BartonSternberg.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/BartonSternberg.html"·title="class·in·jebl.evolution.align">BartonSternberg</a></dt> |
| 2694 | <dd> </dd> | 2694 | <dd> </dd> |
| 2695 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> | 2695 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> |
| 2696 | <dd> </dd> | 2696 | <dd> </dd> |
| 2697 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 2697 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#getScore()"·class="member-name-link">getScore()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> |
| 2698 | <dd> </dd> | 2698 | <dd> </dd> |
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| 4091 | <dd> </dd> | 4091 | <dd> </dd> |
| 4092 | <dt><a·href="jebl/evolution/io/ImportHelper.html#next()"·class="member-name-link">next()</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> | 4092 | <dt><a·href="jebl/evolution/io/ImportHelper.html#next()"·class="member-name-link">next()</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> |
| 4093 | <dd> </dd> | 4093 | <dd> </dd> |
| 4094 | <dt><a·href="jebl/evolution/align/Align.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 4094 | <dt><a·href="jebl/evolution/align/Align.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 4095 | <dd> | 4095 | <dd> |
| 4096 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4096 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4097 | </dd> | 4097 | </dd> |
| 4098 | <dt><a·href="jebl/evolution/align/ | 4098 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html"·title="class·in·jebl.evolution.[·...·truncated·by·diffoscope;·len:·20,·SHA:·316110aa31521f66ab7fd0c9554fc222ea570fbc60de06451f5ca0869ecde70c·...·]LinearSpaceAffine</a></dt> |
| 4099 | <dd> | 4099 | <dd> |
| 4100 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4100 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4101 | </dd> | 4101 | </dd> |
| 4102 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4102 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4103 | <dd> | 4103 | <dd> |
| 4104 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4104 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4105 | </dd> | 4105 | </dd> |
| 4106 | <dt><a·href="jebl/evolution/align/ | 4106 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> |
| 4107 | <dd> | 4107 | <dd> |
| 4108 | <div·class="block">Get·the·next·state·in·the·traceback</div> | 4108 | <div·class="block">Get·the·next·state·in·the·traceback</div> |
| 4109 | </dd> | 4109 | </dd> |
| 4110 | <dt><a·href="jebl/evolution/align/MaximalSegmentPair.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/MaximalSegmentPair.html"·title="class·in·jebl.evolution.align">MaximalSegmentPair</a></dt> | 4110 | <dt><a·href="jebl/evolution/align/MaximalSegmentPair.html#next(jebl.evolution.align.Traceback)"·class="member-name-link">next(Traceback)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/MaximalSegmentPair.html"·title="class·in·jebl.evolution.align">MaximalSegmentPair</a></dt> |
| 4111 | <dd> </dd> | 4111 | <dd> </dd> |
| 4112 | <dt><a·href="jebl/math/Random.html#nextBoolean()"·class="member-name-link">nextBoolean()</a>·-·Static·method·in·class·jebl.math.<a·href="jebl/math/Random.html"·title="class·in·jebl.math">Random</a></dt> | 4112 | <dt><a·href="jebl/math/Random.html#nextBoolean()"·class="member-name-link">nextBoolean()</a>·-·Static·method·in·class·jebl.math.<a·href="jebl/math/Random.html"·title="class·in·jebl.math">Random</a></dt> |
| 4113 | <dd> | 4113 | <dd> |
| Offset 4542, 45 lines modified | Offset 4542, 45 lines modified | ||
| 4542 | <dd> | 4542 | <dd> |
| 4543 | <div·class="block">Initialises·the·matrices·for·the·alignment.</div> | 4543 | <div·class="block">Initialises·the·matrices·for·the·alignment.</div> |
| 4544 | </dd> | 4544 | </dd> |
| 4545 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> | 4545 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 4546 | <dd> </dd> | 4546 | <dd> </dd> |
| 4547 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpace.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpace.html"·title="class·in·jebl.evolution.align">SmithWatermanLinearSpace</a></dt> | 4547 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpace.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpace.html"·title="class·in·jebl.evolution.align">SmithWatermanLinearSpace</a></dt> |
| 4548 | <dd> </dd> | 4548 | <dd> </dd> |
| 4549 | <dt><a·href="jebl/evolution/align/ | 4549 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html"[·...·truncated·by·diffoscope;·len:·52,·SHA:·7645b3af1df93c0fc662dea5d170f21ac6df1b5cb31f89f4c1f4959dfb7a03ea·...·]LinearSpaceAffine</a></dt> |
| 4550 | <dd> </dd> | 4550 | <dd> </dd> |
| 4551 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4551 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4552 | <dd> </dd> | 4552 | <dd> </dd> |
| 4553 | <dt><a·href="jebl/evolution/align/ | 4553 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolutio[·...·truncated·by·diffoscope;·len:·24,·SHA:·27521478537c1d29e09a2c0bed98a973c44646c90e8158def70ca9ff12656dff·...·]</a></dt> |
| 4554 | <dd> </dd> | 4554 | <dd> </dd> |
| 4555 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 4555 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#prepareAlignment(java.lang.String,java.lang.String)"·class="member-name-link">prepareAlignment(String,·String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> |
| 4556 | <dd> </dd> | 4556 | <dd> </dd> |
| 4557 | <dt><a·href="jebl/evolution/align/ProfileCharacter.html#print()"·class="member-name-link">print()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/ProfileCharacter.html"·title="class·in·jebl.evolution.align">ProfileCharacter</a></dt> | 4557 | <dt><a·href="jebl/evolution/align/ProfileCharacter.html#print()"·class="member-name-link">print()</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/ProfileCharacter.html"·title="class·in·jebl.evolution.align">ProfileCharacter</a></dt> |
| 4558 | <dd> </dd> | 4558 | <dd> </dd> |
| 4559 | <dt><a·href="jebl/evolution/align/Output.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Output.html"·title="class·in·jebl.evolution.align">Output</a></dt> | 4559 | <dt><a·href="jebl/evolution/align/Output.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Output.html"·title="class·in·jebl.evolution.align">Output</a></dt> |
| 4560 | <dd> </dd> | 4560 | <dd> </dd> |
| 4561 | <dt><a·href="jebl/evolution/align/SystemOut.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SystemOut.html"·title="class·in·jebl.evolution.align">SystemOut</a></dt> | 4561 | <dt><a·href="jebl/evolution/align/SystemOut.html#print(java.lang.String)"·class="member-name-link">print(String)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SystemOut.html"·title="class·in·jebl.evolution.align">SystemOut</a></dt> |
| 4562 | <dd> </dd> | 4562 | <dd> </dd> |
| 4563 | <dt><a·href="jebl/evolution/align/Align.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 4563 | <dt><a·href="jebl/evolution/align/Align.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 4564 | <dd> | 4564 | <dd> |
| 4565 | <div·class="block">Print·the·matrix·(matrices)·used·to·compute·the·alignment</div> | 4565 | <div·class="block">Print·the·matrix·(matrices)·used·to·compute·the·alignment</div> |
| 4566 | </dd> | 4566 | </dd> |
| 4567 | <dt><a·href="jebl/evolution/align/NeedlemanWunschAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">NeedlemanWunschAffine</a></dt> | 4567 | <dt><a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/OldNeedlemanWunschAffine.html"·title="class·in·jebl.evolution.align">OldNeedlemanWunschAffine</a></dt> |
| 4568 | <dd> | 4568 | <dd> |
| 4569 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4569 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4570 | </dd> | 4570 | </dd> |
| 4571 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpace.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpace.html"·title="class·in·jebl.evolution.align">SmithWatermanLinearSpace</a></dt> | 4571 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpace.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpace.html"·title="class·in·jebl.evolution.align">SmithWatermanLinearSpace</a></dt> |
| 4572 | <dd> | 4572 | <dd> |
| 4573 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4573 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4574 | </dd> | 4574 | </dd> |
| 4575 | <dt><a·href="jebl/evolution/align/ | 4575 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html"·title="class·in·jebl.evolution.al[·...·truncated·by·diffoscope;·len:·18,·SHA:·de110c75e33a185ce86bd61bad810ee102c278559039263ab19a7eaf4a2f45d1·...·]LinearSpaceAffine</a></dt> |
| 4576 | <dd> | 4576 | <dd> |
| 4577 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4577 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4578 | </dd> | 4578 | </dd> |
| 4579 | <dt><a·href="jebl/evolution/align/ | 4579 | <dt><a·href="jebl/evolution/align/NeedlemanWunsch.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NeedlemanWunsch.html"·title="class·in·jebl.evolution.align">NeedlemanWunsch</a></dt> |
| 4580 | <dd> | 4580 | <dd> |
| 4581 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4581 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4582 | </dd> | 4582 | </dd> |
| 4583 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 4583 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#printf(jebl.evolution.align.Output)"·class="member-name-link">printf(Output)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 4584 | <dd> | 4584 | <dd> |
| 4585 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> | 4585 | <div·class="block">Print·matrix·used·to·calculate·this·alignment.</div> |
| 4586 | </dd> | 4586 | </dd> |
| Offset 5107, 15 lines modified | Offset 5107, 15 lines modified | ||
| 5107 | </dd> | 5107 | </dd> |
| 5108 | <dt><a·href="jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)"·class="member-name-link">setEdgeLength(Node,·Node,·double)</a>·-·Method·in·class·jebl.evolution.trees.<a·href="jebl/evolution/trees/SimpleTree.html"·title="class·in·jebl.evolution.trees">SimpleTree</a></dt> | 5108 | <dt><a·href="jebl/evolution/trees/SimpleTree.html#setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)"·class="member-name-link">setEdgeLength(Node,·Node,·double)</a>·-·Method·in·class·jebl.evolution.trees.<a·href="jebl/evolution/trees/SimpleTree.html"·title="class·in·jebl.evolution.trees">SimpleTree</a></dt> |
| 5109 | <dd> | 5109 | <dd> |
| 5110 | <div·class="block">Set·edge·distance·between·two·adjacent·nodes.</div> | 5110 | <div·class="block">Set·edge·distance·between·two·adjacent·nodes.</div> |
| 5111 | </dd> | 5111 | </dd> |
| 5112 | <dt><a·href="jebl/evolution/io/ImportHelper.html#setExpectedInputLength(long)"·class="member-name-link">setExpectedInputLength(long)</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> | 5112 | <dt><a·href="jebl/evolution/io/ImportHelper.html#setExpectedInputLength(long)"·class="member-name-link">setExpectedInputLength(long)</a>·-·Method·in·class·jebl.evolution.io.<a·href="jebl/evolution/io/ImportHelper.html"·title="class·in·jebl.evolution.io">ImportHelper</a></dt> |
| 5113 | <dd> </dd> | 5113 | <dd> </dd> |
| 5114 | <dt><a·href="jebl/evolution/align/ | 5114 | <dt><a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/SmithWatermanLinearSpaceAffine.html"·title="class·in·jebl.evolution.align">SmithW[·...·truncated·by·diffoscope;·len:·7,·SHA:·76f2bb5e20743e27581cd3f55b6c6aa16e615a85539a13f5e89335b75d9074d6·...·]LinearSpaceAffine</a></dt> |
| 5115 | <dd> </dd> | 5115 | <dd> </dd> |
| 5116 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> | 5116 | <dt><a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html#setGapExtend(float)"·class="member-name-link">setGapExtend(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/NonOverlapMultipleLocalAffine.html"·title="class·in·jebl.evolution.align">NonOverlapMultipleLocalAffine</a></dt> |
| 5117 | <dd> </dd> | 5117 | <dd> </dd> |
| 5118 | <dt><a·href="jebl/evolution/align/Align.html#setGapOpen(float)"·class="member-name-link">setGapOpen(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> | 5118 | <dt><a·href="jebl/evolution/align/Align.html#setGapOpen(float)"·class="member-name-link">setGapOpen(float)</a>·-·Method·in·class·jebl.evolution.align.<a·href="jebl/evolution/align/Align.html"·title="class·in·jebl.evolution.align">Align</a></dt> |
| 5119 | <dd> </dd> | 5119 | <dd> </dd> |
| 5120 | <dt><a·href="jebl/evolution/coalescent/ExponentialGrowth.html#setGrowthRate(double)"·class="member-name-link">setGrowthRate(double)</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/ExponentialGrowth.html"·title="class·in·jebl.evolution.coalescent">ExponentialGrowth</a></dt> | 5120 | <dt><a·href="jebl/evolution/coalescent/ExponentialGrowth.html#setGrowthRate(double)"·class="member-name-link">setGrowthRate(double)</a>·-·Method·in·class·jebl.evolution.coalescent.<a·href="jebl/evolution/coalescent/ExponentialGrowth.html"·title="class·in·jebl.evolution.coalescent">ExponentialGrowth</a></dt> |
| 5121 | <dd> | 5121 | <dd> |
| Offset 2422, 15 lines modified | Offset 2422, 15 lines modified | ||
| 2422 | ······get·the·total·number·of·sampling·events. | 2422 | ······get·the·total·number·of·sampling·events. |
| 2423 | ··getSampleCount()·-·Method·in·class·jebl.evolution.coalescent.Intervals | 2423 | ··getSampleCount()·-·Method·in·class·jebl.evolution.coalescent.Intervals |
| 2424 | ······ | 2424 | ······ |
| 2425 | ··getScore()·-·Method·in·class·jebl.evolution.align.Align | 2425 | ··getScore()·-·Method·in·class·jebl.evolution.align.Align |
| 2426 | ······ | 2426 | ······ |
| 2427 | ··getScore()·-·Method·in·class·jebl.evolution.align.OldNeedlemanWunschAffine | 2427 | ··getScore()·-·Method·in·class·jebl.evolution.align.OldNeedlemanWunschAffine |
| 2428 | ······ | 2428 | ······ |
| 2429 | ··getScore()·-·Method·in·class·jebl.evolution.align. | 2429 | ··getScore()·-·Method·in·class·jebl.evolution.align.MaximalSegmentPair |
| 2430 | ······ | 2430 | ······ |
| 2431 | ··getScore()·-·Method·in·class·jebl.evolution.align.BartonSternberg | 2431 | ··getScore()·-·Method·in·class·jebl.evolution.align.BartonSternberg |
| 2432 | ······ | 2432 | ······ |
| 2433 | ··getScore()·-·Method·in·class·jebl.evolution.align.NeedlemanWunsch | 2433 | ··getScore()·-·Method·in·class·jebl.evolution.align.NeedlemanWunsch |
| 2434 | ······ | 2434 | ······ |
| 2435 | ··getScore()·-·Method·in·class·jebl.evolution.align.NeedlemanWunschAffine | 2435 | ··getScore()·-·Method·in·class·jebl.evolution.align.NeedlemanWunschAffine |
| 2436 | ······ | 2436 | ······ |
| Offset 3722, 21 lines modified | Offset 3722, 20 lines modified | ||
| 3722 | ··jebl.evolution.align.TracebackPlotter | 3722 | ··jebl.evolution.align.TracebackPlotter |
| 3723 | ······ | 3723 | ······ |
| 3724 | ··next()·-·Method·in·class·jebl.evolution.io.ImportHelper | 3724 | ··next()·-·Method·in·class·jebl.evolution.io.ImportHelper |
| 3725 | ······ | 3725 | ······ |
| 3726 | ··next(Traceback)·-·Method·in·class·jebl.evolution.align.Align | 3726 | ··next(Traceback)·-·Method·in·class·jebl.evolution.align.Align |
| 3727 | ······Get·the·next·state·in·the·traceback | 3727 | ······Get·the·next·state·in·the·traceback |
| 3728 | ··next(Traceback)·-·Method·in·class | 3728 | ··next(Traceback)·-·Method·in·class |
| 3729 | ··jebl.evolution.align. | 3729 | ··jebl.evolution.align.SmithWatermanLinearSpaceAffine |
| 3730 | ······Get·the·next·state·in·the·traceback | 3730 | ······Get·the·next·state·in·the·traceback |
| 3731 | ··next(Traceback)·-·Method·in·class | 3731 | ··next(Traceback)·-·Method·in·class |
| 3732 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine | 3732 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine |
| 3733 | ······Get·the·next·state·in·the·traceback | 3733 | ······Get·the·next·state·in·the·traceback |
| 3734 | ··next(Traceback)·-·Method·in·class·jebl.evolution.align.NeedlemanWunsch | ||
| 3734 | ··next(Traceback)·-·Method·in·class | ||
| 3735 | ··jebl.evolution.align.SmithWatermanLinearSpace | ||
| 3736 | ······Get·the·next·state·in·the·traceback | 3735 | ······Get·the·next·state·in·the·traceback |
| 3737 | ··next(Traceback)·-·Method·in·class·jebl.evolution.align.MaximalSegmentPair | 3736 | ··next(Traceback)·-·Method·in·class·jebl.evolution.align.MaximalSegmentPair |
| 3738 | ······ | 3737 | ······ |
| 3739 | ··nextBoolean()·-·Static·method·in·class·jebl.math.Random | 3738 | ··nextBoolean()·-·Static·method·in·class·jebl.math.Random |
| 3740 | ······Access·a·default·instance·of·this·class,·access·is·synchronized | 3739 | ······Access·a·default·instance·of·this·class,·access·is·synchronized |
| 3741 | ··nextByte()·-·Static·method·in·class·jebl.math.Random | 3740 | ··nextByte()·-·Static·method·in·class·jebl.math.Random |
| 3742 | ······Access·a·default·instance·of·this·class,·access·is·synchronized | 3741 | ······Access·a·default·instance·of·this·class,·access·is·synchronized |
| Offset 4107, 42 lines modified | Offset 4106, 43 lines modified | ||
| 4107 | ··prepareAlignment(String,_String)·-·Method·in·class | 4106 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4108 | ··jebl.evolution.align.OldNeedlemanWunschAffine | 4107 | ··jebl.evolution.align.OldNeedlemanWunschAffine |
| 4109 | ······ | 4108 | ······ |
| 4110 | ··prepareAlignment(String,_String)·-·Method·in·class | 4109 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4111 | ··jebl.evolution.align.SmithWatermanLinearSpace | 4110 | ··jebl.evolution.align.SmithWatermanLinearSpace |
| 4112 | ······ | 4111 | ······ |
| 4113 | ··prepareAlignment(String,_String)·-·Method·in·class | 4112 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4114 | ··jebl.evolution.align. | 4113 | ··jebl.evolution.align.SmithWatermanLinearSpaceAffine |
| 4115 | ······ | 4114 | ······ |
| 4116 | ··prepareAlignment(String,_String)·-·Method·in·class | 4115 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4117 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine | 4116 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine |
| 4118 | ······ | 4117 | ······ |
| 4119 | ··prepareAlignment(String,_String)·-·Method·in·class | 4118 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4120 | ··jebl.evolution.align. | 4119 | ··jebl.evolution.align.NeedlemanWunsch |
| 4121 | ······ | 4120 | ······ |
| 4122 | ··prepareAlignment(String,_String)·-·Method·in·class | 4121 | ··prepareAlignment(String,_String)·-·Method·in·class |
| 4123 | ··jebl.evolution.align.NeedlemanWunschAffine | 4122 | ··jebl.evolution.align.NeedlemanWunschAffine |
| 4124 | ······ | 4123 | ······ |
| 4125 | ··print()·-·Method·in·class·jebl.evolution.align.ProfileCharacter | 4124 | ··print()·-·Method·in·class·jebl.evolution.align.ProfileCharacter |
| 4126 | ······ | 4125 | ······ |
| 4127 | ··print(String)·-·Method·in·class·jebl.evolution.align.Output | 4126 | ··print(String)·-·Method·in·class·jebl.evolution.align.Output |
| 4128 | ······ | 4127 | ······ |
| 4129 | ··print(String)·-·Method·in·class·jebl.evolution.align.SystemOut | 4128 | ··print(String)·-·Method·in·class·jebl.evolution.align.SystemOut |
| 4130 | ······ | 4129 | ······ |
| 4131 | ··printf(Output)·-·Method·in·class·jebl.evolution.align.Align | 4130 | ··printf(Output)·-·Method·in·class·jebl.evolution.align.Align |
| 4132 | ······Print·the·matrix·(matrices)·used·to·compute·the·alignment | 4131 | ······Print·the·matrix·(matrices)·used·to·compute·the·alignment |
| 4133 | ··printf(Output)·-·Method·in·class | 4132 | ··printf(Output)·-·Method·in·class |
| 4133 | ··jebl.evolution.align.OldNeedlemanWunschAffine | ||
| 4134 | ······Print·matrix·used·to·calculate·this·alignment. | 4134 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4135 | ··printf(Output)·-·Method·in·class | 4135 | ··printf(Output)·-·Method·in·class |
| 4136 | ··jebl.evolution.align.SmithWatermanLinearSpace | 4136 | ··jebl.evolution.align.SmithWatermanLinearSpace |
| 4137 | ······Print·matrix·used·to·calculate·this·alignment. | 4137 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4138 | ··printf(Output)·-·Method·in·class | 4138 | ··printf(Output)·-·Method·in·class |
| 4139 | ··jebl.evolution.align. | 4139 | ··jebl.evolution.align.SmithWatermanLinearSpaceAffine |
| 4140 | ······Print·matrix·used·to·calculate·this·alignment. | 4140 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4141 | ··printf(Output)·-·Method·in·class·jebl.evolution.align. | 4141 | ··printf(Output)·-·Method·in·class·jebl.evolution.align.NeedlemanWunsch |
| 4142 | ······Print·matrix·used·to·calculate·this·alignment. | 4142 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4143 | ··printf(Output)·-·Method·in·class | 4143 | ··printf(Output)·-·Method·in·class |
| 4144 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine | 4144 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine |
| 4145 | ······Print·matrix·used·to·calculate·this·alignment. | 4145 | ······Print·matrix·used·to·calculate·this·alignment. |
| 4146 | ··println()·-·Method·in·class·jebl.evolution.align.Output | 4146 | ··println()·-·Method·in·class·jebl.evolution.align.Output |
| 4147 | ······ | 4147 | ······ |
| 4148 | ··println()·-·Method·in·class·jebl.evolution.align.SystemOut | 4148 | ··println()·-·Method·in·class·jebl.evolution.align.SystemOut |
| Offset 4645, 15 lines modified | Offset 4645, 15 lines modified | ||
| 4645 | ······Change·length·of·an·existing·edge. | 4645 | ······Change·length·of·an·existing·edge. |
| 4646 | ··setEdgeLength(Node,_Node,_double)·-·Method·in·class | 4646 | ··setEdgeLength(Node,_Node,_double)·-·Method·in·class |
| 4647 | ··jebl.evolution.trees.SimpleTree | 4647 | ··jebl.evolution.trees.SimpleTree |
| 4648 | ······Set·edge·distance·between·two·adjacent·nodes. | 4648 | ······Set·edge·distance·between·two·adjacent·nodes. |
| 4649 | ··setExpectedInputLength(long)·-·Method·in·class·jebl.evolution.io.ImportHelper | 4649 | ··setExpectedInputLength(long)·-·Method·in·class·jebl.evolution.io.ImportHelper |
| 4650 | ······ | 4650 | ······ |
| 4651 | ··setGapExtend(float)·-·Method·in·class | 4651 | ··setGapExtend(float)·-·Method·in·class |
| 4652 | ··jebl.evolution.align. | 4652 | ··jebl.evolution.align.SmithWatermanLinearSpaceAffine |
| 4653 | ······ | 4653 | ······ |
| 4654 | ··setGapExtend(float)·-·Method·in·class | 4654 | ··setGapExtend(float)·-·Method·in·class |
| 4655 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine | 4655 | ··jebl.evolution.align.NonOverlapMultipleLocalAffine |
| 4656 | ······ | 4656 | ······ |
| 4657 | ··setGapOpen(float)·-·Method·in·class·jebl.evolution.align.Align | 4657 | ··setGapOpen(float)·-·Method·in·class·jebl.evolution.align.Align |
| 4658 | ······ | 4658 | ······ |
| 4659 | ··setGrowthRate(double)·-·Method·in·class | 4659 | ··setGrowthRate(double)·-·Method·in·class |
| Offset 3880, 15 lines modified | Offset 3880, 15 lines modified | ||
| 3880 | ····"l":·"getScore()" | 3880 | ····"l":·"getScore()" |
| 3881 | },·{ | 3881 | },·{ |
| 3882 | ····"p":·"jebl.evolution.align", | 3882 | ····"p":·"jebl.evolution.align", |
| 3883 | ····"c":·"OldNeedlemanWunschAffine", | 3883 | ····"c":·"OldNeedlemanWunschAffine", |
| 3884 | ····"l":·"getScore()" | 3884 | ····"l":·"getScore()" |
| 3885 | },·{ | 3885 | },·{ |
| 3886 | ····"p":·"jebl.evolution.align", | 3886 | ····"p":·"jebl.evolution.align", |
| 3887 | ····"c":·" | 3887 | ····"c":·"MaximalSegmentPair", |
| 3888 | ····"l":·"getScore()" | 3888 | ····"l":·"getScore()" |
| 3889 | },·{ | 3889 | },·{ |
| 3890 | ····"p":·"jebl.evolution.align", | 3890 | ····"p":·"jebl.evolution.align", |
| 3891 | ····"c":·"BartonSternberg", | 3891 | ····"c":·"BartonSternberg", |
| 3892 | ····"l":·"getScore()" | 3892 | ····"l":·"getScore()" |
| 3893 | },·{ | 3893 | },·{ |
| 3894 | ····"p":·"jebl.evolution.align", | 3894 | ····"p":·"jebl.evolution.align", |
| Offset 5921, 25 lines modified | Offset 5921, 25 lines modified | ||
| 5921 | },·{ | 5921 | },·{ |
| 5922 | ····"p":·"jebl.evolution.align", | 5922 | ····"p":·"jebl.evolution.align", |
| 5923 | ····"c":·"Align", | 5923 | ····"c":·"Align", |
| 5924 | ····"l":·"next(Traceback)", | 5924 | ····"l":·"next(Traceback)", |
| 5925 | ····"u":·"next(jebl.evolution.align.Traceback)" | 5925 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 5926 | },·{ | 5926 | },·{ |
| 5927 | ····"p":·"jebl.evolution.align", | 5927 | ····"p":·"jebl.evolution.align", |
| 5928 | ····"c":·" | 5928 | ····"c":·"SmithWatermanLinearSpaceAffine", |
| 5929 | ····"l":·"next(Traceback)", | 5929 | ····"l":·"next(Traceback)", |
| 5930 | ····"u":·"next(jebl.evolution.align.Traceback)" | 5930 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 5931 | },·{ | 5931 | },·{ |
| 5932 | ····"p":·"jebl.evolution.align", | 5932 | ····"p":·"jebl.evolution.align", |
| 5933 | ····"c":·"NonOverlapMultipleLocalAffine", | 5933 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 5934 | ····"l":·"next(Traceback)", | 5934 | ····"l":·"next(Traceback)", |
| 5935 | ····"u":·"next(jebl.evolution.align.Traceback)" | 5935 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 5936 | },·{ | 5936 | },·{ |
| 5937 | ····"p":·"jebl.evolution.align", | 5937 | ····"p":·"jebl.evolution.align", |
| 5938 | ····"c":·" | 5938 | ····"c":·"NeedlemanWunsch", |
| 5939 | ····"l":·"next(Traceback)", | 5939 | ····"l":·"next(Traceback)", |
| 5940 | ····"u":·"next(jebl.evolution.align.Traceback)" | 5940 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| 5941 | },·{ | 5941 | },·{ |
| 5942 | ····"p":·"jebl.evolution.align", | 5942 | ····"p":·"jebl.evolution.align", |
| 5943 | ····"c":·"MaximalSegmentPair", | 5943 | ····"c":·"MaximalSegmentPair", |
| 5944 | ····"l":·"next(Traceback)", | 5944 | ····"l":·"next(Traceback)", |
| 5945 | ····"u":·"next(jebl.evolution.align.Traceback)" | 5945 | ····"u":·"next(jebl.evolution.align.Traceback)" |
| Offset 6450, 25 lines modified | Offset 6450, 25 lines modified | ||
| 6450 | },·{ | 6450 | },·{ |
| 6451 | ····"p":·"jebl.evolution.align", | 6451 | ····"p":·"jebl.evolution.align", |
| 6452 | ····"c":·"SmithWatermanLinearSpace", | 6452 | ····"c":·"SmithWatermanLinearSpace", |
| 6453 | ····"l":·"prepareAlignment(String,·String)", | 6453 | ····"l":·"prepareAlignment(String,·String)", |
| 6454 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6454 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6455 | },·{ | 6455 | },·{ |
| 6456 | ····"p":·"jebl.evolution.align", | 6456 | ····"p":·"jebl.evolution.align", |
| 6457 | ····"c":·" | 6457 | ····"c":·"SmithWatermanLinearSpaceAffine", |
| 6458 | ····"l":·"prepareAlignment(String,·String)", | 6458 | ····"l":·"prepareAlignment(String,·String)", |
| 6459 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6459 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6460 | },·{ | 6460 | },·{ |
| 6461 | ····"p":·"jebl.evolution.align", | 6461 | ····"p":·"jebl.evolution.align", |
| 6462 | ····"c":·"NonOverlapMultipleLocalAffine", | 6462 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 6463 | ····"l":·"prepareAlignment(String,·String)", | 6463 | ····"l":·"prepareAlignment(String,·String)", |
| 6464 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6464 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6465 | },·{ | 6465 | },·{ |
| 6466 | ····"p":·"jebl.evolution.align", | 6466 | ····"p":·"jebl.evolution.align", |
| 6467 | ····"c":·" | 6467 | ····"c":·"NeedlemanWunsch", |
| 6468 | ····"l":·"prepareAlignment(String,·String)", | 6468 | ····"l":·"prepareAlignment(String,·String)", |
| 6469 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6469 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| 6470 | },·{ | 6470 | },·{ |
| 6471 | ····"p":·"jebl.evolution.align", | 6471 | ····"p":·"jebl.evolution.align", |
| 6472 | ····"c":·"NeedlemanWunschAffine", | 6472 | ····"c":·"NeedlemanWunschAffine", |
| 6473 | ····"l":·"prepareAlignment(String,·String)", | 6473 | ····"l":·"prepareAlignment(String,·String)", |
| 6474 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" | 6474 | ····"u":·"prepareAlignment(java.lang.String,java.lang.String)" |
| Offset 6489, 30 lines modified | Offset 6489, 30 lines modified | ||
| 6489 | },·{ | 6489 | },·{ |
| 6490 | ····"p":·"jebl.evolution.align", | 6490 | ····"p":·"jebl.evolution.align", |
| 6491 | ····"c":·"Align", | 6491 | ····"c":·"Align", |
| 6492 | ····"l":·"printf(Output)", | 6492 | ····"l":·"printf(Output)", |
| 6493 | ····"u":·"printf(jebl.evolution.align.Output)" | 6493 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6494 | },·{ | 6494 | },·{ |
| 6495 | ····"p":·"jebl.evolution.align", | 6495 | ····"p":·"jebl.evolution.align", |
| 6496 | ····"c":·"NeedlemanWunschAffine", | 6496 | ····"c":·"OldNeedlemanWunschAffine", |
| 6497 | ····"l":·"printf(Output)", | 6497 | ····"l":·"printf(Output)", |
| 6498 | ····"u":·"printf(jebl.evolution.align.Output)" | 6498 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6499 | },·{ | 6499 | },·{ |
| 6500 | ····"p":·"jebl.evolution.align", | 6500 | ····"p":·"jebl.evolution.align", |
| 6501 | ····"c":·"SmithWatermanLinearSpace", | 6501 | ····"c":·"SmithWatermanLinearSpace", |
| 6502 | ····"l":·"printf(Output)", | 6502 | ····"l":·"printf(Output)", |
| 6503 | ····"u":·"printf(jebl.evolution.align.Output)" | 6503 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6504 | },·{ | 6504 | },·{ |
| 6505 | ····"p":·"jebl.evolution.align", | 6505 | ····"p":·"jebl.evolution.align", |
| 6506 | ····"c":·" | 6506 | ····"c":·"SmithWatermanLinearSpaceAffine", |
| 6507 | ····"l":·"printf(Output)", | 6507 | ····"l":·"printf(Output)", |
| 6508 | ····"u":·"printf(jebl.evolution.align.Output)" | 6508 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6509 | },·{ | 6509 | },·{ |
| 6510 | ····"p":·"jebl.evolution.align", | 6510 | ····"p":·"jebl.evolution.align", |
| 6511 | ····"c":·" | 6511 | ····"c":·"NeedlemanWunsch", |
| 6512 | ····"l":·"printf(Output)", | 6512 | ····"l":·"printf(Output)", |
| 6513 | ····"u":·"printf(jebl.evolution.align.Output)" | 6513 | ····"u":·"printf(jebl.evolution.align.Output)" |
| 6514 | },·{ | 6514 | },·{ |
| 6515 | ····"p":·"jebl.evolution.align", | 6515 | ····"p":·"jebl.evolution.align", |
| 6516 | ····"c":·"NonOverlapMultipleLocalAffine", | 6516 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 6517 | ····"l":·"printf(Output)", | 6517 | ····"l":·"printf(Output)", |
| 6518 | ····"u":·"printf(jebl.evolution.align.Output)" | 6518 | ····"u":·"printf(jebl.evolution.align.Output)" |
| Offset 7277, 15 lines modified | Offset 7277, 15 lines modified | ||
| 7277 | ····"u":·"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)" | 7277 | ····"u":·"setEdgeLength(jebl.evolution.graphs.Node,jebl.evolution.graphs.Node,double)" |
| 7278 | },·{ | 7278 | },·{ |
| 7279 | ····"p":·"jebl.evolution.io", | 7279 | ····"p":·"jebl.evolution.io", |
| 7280 | ····"c":·"ImportHelper", | 7280 | ····"c":·"ImportHelper", |
| 7281 | ····"l":·"setExpectedInputLength(long)" | 7281 | ····"l":·"setExpectedInputLength(long)" |
| 7282 | },·{ | 7282 | },·{ |
| 7283 | ····"p":·"jebl.evolution.align", | 7283 | ····"p":·"jebl.evolution.align", |
| 7284 | ····"c":·" | 7284 | ····"c":·"SmithWatermanLinearSpaceAffine", |
| 7285 | ····"l":·"setGapExtend(float)" | 7285 | ····"l":·"setGapExtend(float)" |
| 7286 | },·{ | 7286 | },·{ |
| 7287 | ····"p":·"jebl.evolution.align", | 7287 | ····"p":·"jebl.evolution.align", |
| 7288 | ····"c":·"NonOverlapMultipleLocalAffine", | 7288 | ····"c":·"NonOverlapMultipleLocalAffine", |
| 7289 | ····"l":·"setGapExtend(float)" | 7289 | ····"l":·"setGapExtend(float)" |
| 7290 | },·{ | 7290 | },·{ |
| 7291 | ····"p":·"jebl.evolution.align", | 7291 | ····"p":·"jebl.evolution.align", |